This is just standard modeling, nothing to stress over.
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If you want something to be different... it has to BE different...in ArchiCAD. Artlantis gives you some flexibility, but not over slab areas.
If certain walls are supposed to have a different material/color, then you must model them that way. If the slabs in certain room need to have different finishes... then they must be unique slabs. A common solution is to have a structural slab, and then to magic-wand a thin veneer slab within a room with the room's floor finish. The veneer slab will not be dynamic, unfortunately... so if you move walls, you'll have to resize or re-magic wand your 'finish' slab(s).
Glass being re-assigned globally in Artlantis is a standard thing for when you export by material. All things of the same material will be selected by default. The assumption is that if you called it 'glass' in AC, it is all supposed to be the same.
You have two options. First, you can use different glass materials in AC, assigned to elements that are supposed to be treated similarly. Make duplicates of your AC glass material, and assign one to your cutain walls, one to your doors, etc - however you anticipate wanting different shaders in Artlantis.
Alternatively... you can re-assign surfaces in Artlantis. Sometimes this is the easiest method (just a surface here and there) - sometimes it is more tedious than going back to AC and breaking up the materials with different names. With the Shader inspector open, use the arrow tool and its options to select and assign a new material to any surface you want. See Artlantis tutorials.
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